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CONCEPT 1.0 data

This repository contains data and scripts used to make all figures included in the paper ‘The cosmological simulation code CONCEPT 1.0’, which is the primary code paper for the CONCEPT code.

power spectra

Generating figures

The figures (already present in the figure directory) can be regenerated by running

python=/path/to/python make

where /path/to/python is the path to the Python interpreter to use.

This will fist parse and process the raw data files and store the results in a pickled format in a .pickle directory (if generating the figures once more, this pickled data will be used directly). The figures are then created from the processed data.

Cleanup

  • The generated figures can be removed via 
    make clean-figure
  • The pickled data can be removed via 
    make clean-pickle
  • The figures as well as the pickled data can be simultaneously removed via 
    make clean

Note that figure/abspower.png (displayed within this README) will not be removed by any of these.

Required libraries and tools

The figure generation requires the following libraries and tools to be installed on the system. With the exception of Python, all need to be located on PATH. The version numbers given are known to work, though many other versions will work as well.

  • Python 3.9.9
    • NumPy 1.20.3, 1.21.4
    • SciPy 1.7.3
    • Matplotlib 3.5.0
    • CLASS 2.7.2
    • Noise 1.2.2
  • LaTeX, e.g. TeX Live 2019.20200218-1 (Ubuntu: sudo apt install texlive-full)
  • Ghostscript 9.50 (Ubuntu: sudo apt install ghostscript)
  • pdfcrop 1.38 (Ubuntu: sudo apt install texlive-extra-utils)
  • pdfinfo 0.86.1 (Ubuntu: sudo apt install poppler-utils)
  • (GNU) Bash 5.0.17
  • (GNU) Make 4.2.1
  • (GNU) grep 3.4
  • GNU coreutils 8.30

The above versions of Python itself and Python packages coincide with the versions shipping with CONCEPT 1.0.1. If you have this version of CONCEPT installed, you may then use its Python distribution to build the figures. You will however still need to install the Noise package:

(source concept && $python -m pip install noise==1.2.2)

Data

The raw data (situated within the data directory) consists of

  • Power spectrum data files of CONCEPT, GADGET-2 and GADGET-4 simulations, all computed via CONCEPT.
  • Log files of CONCEPT and GADGET-2 simulations.
  • Memory dumps.
    • These are generated via the memdump script. Though not needed to generate the figures, this script is nontheless included in the script directory for completeness.
  • The file t_a.dat mapping cosmic times (in Gyr) and scale factor values to each other, in a radiation-less cosmology with H0 = 67*km/(s*Mpc), Ωb = 0.049, Ωcdm = 0.27, which is used for all simulations.

Scripts

The scripts (in the script directory) consist of a .py file for each figure. The helper.py file provides functionality common to the other .py files. The generate script calls each of the .py files responsible for a figure, after which it compresses the generated PDF.

As mentioned above, an additional memdump script is also present, though this not used for the figure generation. The memory usage data has been recorded using this script, which is able to accurately measure the total memory usage of a Slurm job across multiple compute nodes.

Disclaimer: All scripts in this repository are written for their singular purpose. Little attempt has been made to properly document, structure, generalise or clean them up.

Replicating simulations

In addition to the data produced from running simulations, we further provide simulation parameter files (and more) for reproducing these simulations. Such files files are located in the param directory and include

  • concept: This is a single CONCEPT parameter file capable of running any of the CONCEPT simulations used for the figures. How to use this parameter file is documented within itself. This parameter file is also capable of producing the initial condition snapshots (used for both CONCEPT and GADGET simulations). By default, the parameters of this file are chosen as to reproduce Figure 4.
  • gadget2: This is a directory containing a GADGET-2 parameter file param, a GADGET-2 Makefile as well as an outputlist of scale factor values at which do dump snapshots (not including the initial and final value). Together, these result in a GADGET-2 simulation corresponding to Figure 4, or equivalently the 'standard' precision lines of the lower left panel of Figure 5, when combined with the results of the CONCEPT simulation. With familiarity of GADGET-2 it should be trivial to adapt these files for GADGET-2 simulations used for other plots as well.
  • gadget4: This is a directory containing a GADGET-4 parameter file param, a GADGET-4 configuration file Config.sh as well as the same outputlist as included for GADGET-2. Together, these result in a GADGET-4 simulation corresponding to the TreePM (O5) lines of Figure 6, when combined with the results of the CONCEPT simulation. With familiarity of GADGET-4 it should be trivial to adapt these files for the other GADGET-4 lines shown in Figure 6.

While the CONCEPT simulations are set up to dump power spectra directly, both GADGET-2 and GADGET-4 will dump snapshots. To compute power spectra from these snapshots, use the CONCEPT powerspec utility:

./concept -u powerspec /path/to/gadget-snapshot -p /path/to/this/repo/param/concept

where the supplied CONCEPT parameter file supplies the power spectrum settings. You are advised to further supply a decent number of processes (-n) and probably submit the power spectrum computation as a remote job (-q). See the CONCEPT documentation for details, in particular the tutorial section about comparisons between CONCEPT and GADGET-2, which also demonstrates how one can automatically generate the GADGET-2 parameter and Makefile from the CONCEPT parameter file.

The specific code versions used to generate the data included in this repository are CONCEPT 1.0.0, GADGET 2.0.7 and Git commit 8a10478b3e62d202808407e40a5f94a8b5e88d80 of GADGET-4.

The values of physical constants within the GADGET-2 and GADGET-4 codes have been slightly adjusted to match the values used within CONCEPT 1.0. The adjusted values are as follows.

  • GADGET-2, allvars.h: 
    #define GRAVITY          6.6743e-08
#define SOLAR_MASS       1.98841e+33
#define C                29979245800.0
#define PLANCK           6.62607015e-27
#define CM_PER_MPC       3.0856775814913676e+24
#define HUBBLE           3.2407792894443648e-18
#define SEC_PER_MEGAYEAR 3.15576e+13
#define SEC_PER_YEAR     31557600.0
  • GADGET-4, constants.h: 
    #define GRAVITY    6.6743e-08
#define SOLAR_MASS 1.98841e+33
#define PARSEC     3.0856775814913676e+18
#define HUBBLE     3.2407792894443648e-18

If using the GADGET-2 that comes with CONCEPT, these adjustment are already in place.

As stated, by default the parameter files are set up to reproduce Figure 4 (as well as parts of Figures 5 and 6). For this, only a single initial condition snapshot needs to be generated (handled by the CONCEPT parameter file). In order to obtain exactly the same particle realisation as used for the corresponding data included in this repository, you must use a NumPy version below 1.21, due to a change to the way random Rayleigh numbers are constructed. Thus, if you use CONCEPT 1.0 and wants to exactly replicate the power spectra included in this repository, make sure to first downgrade to e.g. NumPy 1.20.3:

(source concept && $python -m pip install numpy==1.20.3)

Note that though all CONCEPT simulations used for the figures can be replicated using the provided CONCEPT parameter file, figures showing statistics internal to the code are not trivially reproducible, as these typically require print-outs of said statistics to be placed within the code, or external monitoring of the program while it is running.

Keeping this Git repository sane

If you clone this repository and regenerate the figures, Git will claim that these have changed:

python=/path/to/python make
git status

However (unless something has gone wrong), only the meta data inside these PDFs will have changed:

git diff --text figure/*.pdf

We thus do not want to include changes to the PDFs as actual changes to the repository. However, since the PDFs are committed as part of the repository, adding them to .gitignore will not help. Instead do the following:

git update-index --assume-unchanged figure/*.pdf